@article {119,
	title = {Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells.},
	journal = {Cell},
	volume = {184},
	year = {2021},
	month = {2021 01 07},
	pages = {92-105.e16},
	abstract = {<p>To better understand host-virus genetic dependencies and find potential therapeutic targets for COVID-19, we performed a genome-scale CRISPR loss-of-function screen to identify host factors required for SARS-CoV-2 viral infection of human alveolar epithelial cells. Top-ranked genes cluster into distinct pathways, including the vacuolar ATPase proton pump, Retromer, and Commander complexes. We validate these gene targets using several orthogonal methods such as CRISPR knockout, RNA interference knockdown, and small-molecule inhibitors. Using single-cell RNA-sequencing, we identify shared transcriptional changes in cholesterol biosynthesis upon loss of top-ranked genes. In addition, given the key role of the ACE2 receptor in the early stages of viral entry, we show that loss of RAB7A reduces viral entry by sequestering the ACE2 receptor inside cells. Overall, this work provides a genome-scale, quantitative resource of the impact of the loss of each host gene on fitness/response to viral infection.</p>},
	keywords = {A549 Cells, Alveolar Epithelial Cells, Angiotensin-Converting Enzyme 2, Biosynthetic Pathways, Cholesterol, Clustered Regularly Interspaced Short Palindromic Repeats, COVID-19, Endosomes, Gene Expression Profiling, Gene Knockdown Techniques, Gene Knockout Techniques, Genome-Wide Association Study, Host-Pathogen Interactions, Humans, rab GTP-Binding Proteins, rab7 GTP-Binding Proteins, RNA Interference, SARS-CoV-2, Single-Cell Analysis, Viral Load},
	issn = {1097-4172},
	doi = {10.1016/j.cell.2020.10.030},
	author = {Daniloski, Zharko and Jordan, Tristan X and Wessels, Hans-Hermann and Hoagland, Daisy A and Kasela, Silva and Legut, Mateusz and Maniatis, Silas and Mimitou, Eleni P and Lu, Lu and Geller, Evan and Danziger, Oded and Rosenberg, Brad R and Phatnani, Hemali and Smibert, Peter and Lappalainen, Tuuli and tenOever, Benjamin R and Sanjana, Neville E}
}
@article {26,
	title = {Simultaneous epitope and transcriptome measurement in single cells.},
	journal = {Nat Methods},
	volume = {14},
	year = {2017},
	month = {2017 Sep},
	pages = {865-868},
	abstract = {<p>High-throughput single-cell RNA sequencing has transformed our understanding of complex cell populations, but it does not provide phenotypic information such as cell-surface protein levels. Here, we describe cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq), a method in which oligonucleotide-labeled antibodies are used to integrate cellular protein and transcriptome measurements into an efficient, single-cell readout. CITE-seq is compatible with existing single-cell sequencing approaches and scales readily with throughput increases.</p>},
	keywords = {Epitope Mapping, Epitopes, Gene Expression Profiling, High-Throughput Nucleotide Sequencing, Sequence Analysis, RNA, Tissue Array Analysis, Transcriptome},
	issn = {1548-7105},
	doi = {10.1038/nmeth.4380},
	author = {Stoeckius, Marlon and Hafemeister, Christoph and Stephenson, William and Houck-Loomis, Brian and Chattopadhyay, Pratip K and Swerdlow, Harold and Satija, Rahul and Smibert, Peter}
}
